Ecm tuning questions

Ok took my truck to the cummins place to bump the hp and tq..they plug it up get all the information out they need..tell me it's set at 280hp which I knew and 1100tq. I'm like what the ...should be at 1250tq what it was supposed to be factory settings at ..I had a new Ecm put on in 2009 the same place did it but sent the old Ecm out before pulling the info out of it..so thatstop irritating knowing they didn't set it back right ..the tag is on the motor with specs ..
So I'm there from 11am til about 230 300pm then they come out and say we can't program it from inside the truck the port is not letting use do it..the port under the hood has no power so we must pull everything out the way and pull the Ecm to program it..I'm like ok hummm ..cause this adds more hrs and money ..my question is how can you pull all the information out with that port in the truck which they said they would use to reprogram the Ecm but can't reprogram it from there...does this sound right ....am I missing something . ..any help would be appreciated . .97 freightliner fld cummins m11celect plus

 

That's about what I was thinking . .you can pull information from there but can't program . .pull ecm few more hrs of labor smh

 

Thanks that's makes sense . .but that's where they program it from last time..inside the truck . .is it a hassle to take the ecm out myself ..I mean is it more the just the plugs into see on it..